The role of the circadian transcriptional network in the aging Drosophila eye

The circadian rhythm controls 24-hour periodic behaviors and physiology, and is observed across animal kingdoms including animals, plants, and fungi. The circadian clock is synchronized with the solar day, maintaining a robust 24-hour periodicity in consistent environmental conditions. Despite this robustness, behaviors that desynchronize the circadian clock with the solar day (e.g., shift working, sleep deprivation) have been widely implicated as being detrimental to human health. Additionally, the circadian rhythm in humans shows both an altered phase and a decrease in amplitude with aging. The circadian clock is synchronized by light at the highest level via direct innervation from the eyes to the suprachiasmatic nucleus in the hypothalamus. During aging, visual function decreases, which can result in decreased circadian photoreception, linking loss in visual function with decreased circadian rhythmicity. Despite these links between aging, alterations in circadian rhythm, and age-related decline in visual function, much remains unknown about the complex interplay between these processes. To profile transcriptome-wide rhythmic changes in photoreceptors during aging, photoreceptor nuclei were collected from young (D10) and old (D50) flies every four hours and used for nuclear RNA-seq. Overall design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.